Journal Article

Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity

Oakes, Melanie, Sandmeyer, Suzanne, Yu, James, Kanomata, Yuzo, Baldi, Pierre, Wu, Jenny, Jahn, Ethan, Magnan, Christophe, Chang, Ivan, Zeller, Michael

2016

Overview

Yarrowia lipolytica, an oleaginous yeast, is capable of accumulating significant cellular mass in lipid making it an important source of biosustainable hydrocarbon-based chemicals. In spite of a similar number of protein-coding genes to that in other Hemiascomycetes, the Y. lipolytica genome is almost double that of model yeasts. Despite its economic importance and several distinct strains in common use, an independent genome assembly exists for only one strain. We report here a de novo annotated assembly of the chromosomal genome of an industrially-relevant strain, W29/CLIB89, determined by hybrid next-generation sequencing. For the first time, each Y. lipolytica chromosome is represented by a single contig. The telomeric rDNA repeats were localized by Irys long-range genome mapping and one complete copy of the rDNA sequence is reported. Two large structural variants and retroelement differences with reference strain CLIB122 including a full-length, novel Ty3/Gypsy long terminal repeat (LTR) retrotransposon and multiple LTR-like sequences are described. Strikingly, several of these are adjacent to RNA polymerase III-transcribed genes, which are almost double in number in Y. lipolytica compared to other Hemiascomycetes. In addition to previously-reported dimeric RNA polymerase III-transcribed genes, tRNA pseudogenes were identified. Multiple full-length and truncated LINE elements are also present. Therefore, although identified transposons do not constitute a significant fraction of the Y. lipolytica genome, they could have played an active role in its evolution. Differences between the sequence of this strain and of the existing reference strain underscore the utility of an additional independent genome assembly for this economically important organism.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Acids / Addition polymerization / Analysis / Assembly / Baking yeast / Base Sequence / Bioinformatics / Biology and Life Sciences / Chromosomes / Chromosomes, Fungal - genetics / Computer science / Data bases / DNA Transposable Elements - genetics / DNA-directed RNA polymerase / Economic importance / Economic models / Gene mapping / Gene sequencing / Genes / Genes, Bacterial / Genetic Variation / Genomes / Genomics / Hydrocarbons / Long interspersed nucleotide elements / Long terminal repeat / Medicine / Molecular Sequence Annotation / Nucleotide sequence / Polymerase / Pseudogenes / Research and Analysis Methods / Retroelements / Ribonucleic acid / RNA / Saccharomyces cerevisiae / Sequence Analysis, DNA / Terminal Repeat Sequences - genetics / Transfer RNA / Transposons / tRNA / Yarrowia - genetics / Yarrowia lipolytica / Yeast / Yeasts